scPDB - 1jtu entry

Protein Data Bank Entry:

PDB ID : 1jtu

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2001-08-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thymidylate synthase
ID:	TYSY_ECOLI
AC:	P0A884
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	98 %
B	2 %

Ligand binding site composition:

B-Factor:	33.516
Number of residues:	46
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:	UMP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.206	506.250

% Hydrophobic	% Polar
58.67	41.33
According to VolSite

Ligand :

HET Code:	LYB
Formula:	C35H37N8O15
Molecular weight:	809.713 g/mol
DrugBank ID:	DB02223
Buried Surface Area:	43.49 %
Polar Surface area:	400.32 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	2
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	24

Mass center Coordinates

X	Y	Z
13.7152	10.5074	37.3531

Binding mode :

What is Poseview ?

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C28	CB	HIS- 51	4.41	0	Hydrophobic	false
O8	NH2	ARG- 53	3.15	163.25	H-Bond (Protein Donor)	false
O8	CZ	ARG- 53	3.79	0	Ionic (Protein Cationic)	false
C13	CG2	ILE- 79	4.33	0	Hydrophobic	false
C11	CB	ILE- 79	3.89	0	Hydrophobic	false
C8	CZ2	TRP- 80	4.39	0	Hydrophobic	false
C9	CE2	TRP- 80	4.31	0	Hydrophobic	false
N1	OD2	ASP- 169	3.05	149.85	H-Bond (Ligand Donor)	false
N4	OD2	ASP- 169	3.18	140.74	H-Bond (Ligand Donor)	false
C13	CG	LEU- 172	4.36	0	Hydrophobic	false
C19	CZ	PHE- 176	4.07	0	Hydrophobic	false
C12	CG1	VAL- 262	4.21	0	Hydrophobic	false
N4	O	ALA- 263	3.05	158.1	H-Bond (Ligand Donor)	false
C8	C5	UMP- 565	3.69	0	Hydrophobic	false
O2	O	HOH- 664	3.07	154.2	H-Bond (Protein Donor)	false
O4	O	HOH- 684	2.67	164.61	H-Bond (Protein Donor)	false
N2	O	HOH- 742	2.78	138.05	H-Bond (Protein Donor)	false